> prokaryotes have been around a lot longer, so they’ve had a lot more evolutionary time to find perfect proteins for their perfect little uses.

I'm not sure that adds up: It's not that much longer - 500 million years out of ~3.5 billion?

And the evidence shows that Eukaryotes have evolved much faster and further - just look at the Eukaryota domain. And IIRC part of the reason is advantages such as 'sexual' [0] reproduction - rather than just splitting and (cloning?) DNA, combining chromosomes from two parents.

[0] If that's the correct term.